The purpose of this research is to contribute to the understanding of the dynamics of protein folding by carrying out theoretical studies that develop methods for predicting the folded conformation of a protein in a given environment and the characteristics of transitions among the conformations. The research is divided into two parts: I. Applications of the Diffusion-Collision Model including model studies of the kinetics of Alpha-helix, Beta-sheet packing in folding proteins; a study of the bimolecular kinetics of glucagon self association, protein fragment and protein-nucleic acid interactions; multimicrodomain folding kinetics of myoglobin and Lambda-phage repressor operator binding domain; and Beta-sheet protein folding kinetics. II. Simulation Studies of Secondary Structure Interactions using a simplified model of a polypeptide chain including helix-helix interactions with and without an intervening helical segment; properties of specific helix-helix interactions using pairs of helices from myoglobin and repressor; Beta-strand-Beta-strand interactions with and without an intervening Alpha-helical segment; stochastic dynamics of interacting rigid helices.